Merge branch 'master' of github.com:scalableminds/webknossos into rea…

…ct-17

.gitignore

@@ -77,3 +77,6 @@ coverage-ts
 temp-webknossos-schema**
 conf/application.conf-e
 .env
+.bloop
+.metals
+metals.sbt

CHANGELOG.released.md

@@ -7,6 +7,73 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Calendar Versioning](http://calver.org/) `0Y.0M.MICRO`.
 For upgrade instructions, please check the [migration guide](MIGRATIONS.released.md).
 
+## [24.07.0](https://github.com/scalableminds/webknossos/releases/tag/24.07.0) - 2024-07-05
+[Commits](https://github.com/scalableminds/webknossos/compare/24.06.0...24.07.0)
+
+### Highlights
+- Owners can lock explorative annotations now. Locked annotations cannot be modified by any user. An annotation can be locked in the annotations table and when viewing the annotation via the navbar dropdown menu. [#7801](https://github.com/scalableminds/webknossos/pull/7801)
+- Added the ability to change the unit of the dataset voxel size to any supported unit of the [ome/ngff standard](https://github.com/ome/ngff/blob/39605eec64ceff481bb3a98f0adeaa330ab1ef26/latest/index.bs#L192). This allows users to upload and work with low-resolution datasets with a different base unit than nanometer. [#7783](https://github.com/scalableminds/webknossos/pull/7783)
+
+### Added
+- Added that proofreading merge actions reuse custom names of segments. A merge action now combines the potenial existing custom names of both segments and a split-action copies the custom name to the split-off segment. [#7877](https://github.com/scalableminds/webknossos/pull/7877)
+- Added the option to set a default mapping for a dataset in the dataset view configuration. The default mapping is loaded when the dataset is opened and the user / url does not configure something else. [#7858](https://github.com/scalableminds/webknossos/pull/7858)
+- Uploading an annotation into a dataset that it was not created for now also works if the dataset is in a different organization. [#7816](https://github.com/scalableminds/webknossos/pull/7816)
+- When downloading + reuploading an annotation that is based on a segmentation layer with active mapping, that mapping is now still selected after the reupload. [#7822](https://github.com/scalableminds/webknossos/pull/7822)
+- In the Voxelytics workflow list, the name of the WEBKNOSSOS user who started the job is displayed. [#7794](https://github.com/scalableminds/webknossos/pull/7795)
+- Start an alignment job (aligns the section in a dataset) via the "AI Analysis" button (not available to all users yet). [#7820](https://github.com/scalableminds/webknossos/pull/7820)
+- Added additional validation for the animation job modal. Bounding boxes must be larger then zero. [#7883](https://github.com/scalableminds/webknossos/pull/7883)
+
+### Changed
+- The "WEBKNOSSOS Changelog" modal now lazily loads its content potentially speeding up the initial loading time of WEBKNOSSOS and thus improving the UX. [#7843](https://github.com/scalableminds/webknossos/pull/7843)
+- Updated the min / max settings for the histogram to allow floating point color layers to have negative min / max values. [#7873](https://github.com/scalableminds/webknossos/pull/7873)
+- Made the login, registration, forgot password and dataset dashboard pages more mobile friendly. [#7876](https://github.com/scalableminds/webknossos/pull/7876)
+- From now on only project owner get a notification email upon project overtime. The organization specific email list `overTimeMailingList` was removed. [#7842](https://github.com/scalableminds/webknossos/pull/7842)
+- Replaced skeleton comment tab component with antd's `<Tree />`component. [#7802](https://github.com/scalableminds/webknossos/pull/7802)
+- Updated Typescript to version 5.5.0. [#7878](https://github.com/scalableminds/webknossos/pull/7878)
+
+### Fixed
+- Fixed a bug where the warning to zoom in to see the agglomerate mapping was shown to the user even when the 3D viewport was maximized and no volume data was shown. [#7865](https://github.com/scalableminds/webknossos/issues/7865)
+- Fixed a bug that prevented saving new dataset settings. [#7903](https://github.com/scalableminds/webknossos/pull/7903)
+- Fixed that on large screens the login forms were not horizontally centered. [#7909](https://github.com/scalableminds/webknossos/pull/7909)
+- Fixed a bug where brushing on a fallback segmentation with active mapping and with segment index file would lead to failed saves. [#7833](https://github.com/scalableminds/webknossos/pull/7833)
+- Fixed a bug where the "Hide Meshes" / "Show Meshes" options of the context menu for segment groups were not available although at leas one mesh was set to visible / invisible. [#7890](https://github.com/scalableminds/webknossos/pull/7890)
+- Fixed a bug where sometimes old mismatching javascript code would be served after upgrades. [#7854](https://github.com/scalableminds/webknossos/pull/7854)
+- Fixed a bug where dataset uploads of zipped tiff data via the UI would be rejected. [#7856](https://github.com/scalableminds/webknossos/pull/7856)
+- Fixed a bug with incorrect validation of layer names in the animation modal. [#7882](https://github.com/scalableminds/webknossos/pull/7882)
+- Fixed a bug in the fullMesh.stl route used by the render_animation worker job, where some meshes in proofreading annotations could not be loaded. [#7887](https://github.com/scalableminds/webknossos/pull/7887)
+- Fixed that dataset composition did not work when selecting only one dataset for composition. [#7889](https://github.com/scalableminds/webknossos/pull/7889)
+
+### Removed
+- REST API versions 1 and 2 are no longer supported. Current is 7. [#7783](https://github.com/scalableminds/webknossos/pull/7783)
+- If the datasource-properties.json file for a dataset is missing or contains errors, WEBKNOSSOS no longer attempts to guess its contents from the raw data. Exploring remote datasets will still create the file. [#7697](https://github.com/scalableminds/webknossos/pull/7697)
+
+
+## [24.06.0](https://github.com/scalableminds/webknossos/releases/tag/24.06.0) - 2024-05-27
+[Commits](https://github.com/scalableminds/webknossos/compare/24.05.0...24.06.0)
+
+### Highlights
+- Within the proofreading tool, the user can now interact with the super voxels of a mesh in the 3D viewport. For example, this allows to merge or cut super voxels from another. As before, the proofreading tool requires an agglomerate file. [#7742](https://github.com/scalableminds/webknossos/pull/7742)
+- In the time tracking view, all annotations and tasks can be shown for each user by expanding the table. The individual time spans spent with a task or annotating an explorative annotation can be accessed via CSV export. The detail view including a chart for the individual spans has been removed. [#7733](https://github.com/scalableminds/webknossos/pull/7733)
+
+### Added
+- Minor improvements for the timetracking overview (faster data loading, styling). [#7789](https://github.com/scalableminds/webknossos/pull/7789)
+- Updated several backend dependencies for optimized stability and performance. [#7782](https://github.com/scalableminds/webknossos/pull/7782)
+- Voxelytics workflows can be searched by name and hash. [#7790](https://github.com/scalableminds/webknossos/pull/7790)
+- If a self-hosted WEBKNOSSOS instance has not been updated for six months or more, a closable banner proposes an upgrade to webknossos.org. [#7768](https://github.com/scalableminds/webknossos/pull/7768)
+
+### Changed
+- Non-admin or -manager users can no longer start long-running jobs that create datasets. This includes annotation materialization and AI inferrals. [#7753](https://github.com/scalableminds/webknossos/pull/7753)
+- The config value `datastore.localFolderWhitelist` can now be set for each datastore individually. [#7800](https://github.com/scalableminds/webknossos/pull/7800)
+
+### Fixed
+- Fixed a bug where a toast that was reopened had a flickering effect during the reopening animation. [#7793](https://github.com/scalableminds/webknossos/pull/7793)
+- Fixed a bug where some annotation times would be shown double. [#7787](https://github.com/scalableminds/webknossos/pull/7787)
+- Fixed a bug where no columns were shown in the time tracking overview. [#7803](https://github.com/scalableminds/webknossos/pull/7803)
+- Fixed a bug where ad-hoc meshes for coarse magnifications would have gaps. [#7799](https://github.com/scalableminds/webknossos/pull/7799)
+- Fixed that the context menu didn't open correctly in the 3D viewport when right-clicking a node. [#7809](https://github.com/scalableminds/webknossos/pull/7809)
+- Fixed that right-clicking a mesh in the 3D viewport did crash when the corresponding segmentation layer was not visible. [#7811](https://github.com/scalableminds/webknossos/pull/7811)
+
+
 ## [24.05.0](https://github.com/scalableminds/webknossos/releases/tag/24.05.0) - 2024-04-29
 [Commits](https://github.com/scalableminds/webknossos/compare/24.04.0...24.05.0)
 

CHANGELOG.unreleased.md

@@ -8,29 +8,15 @@ and this project adheres to [Calendar Versioning](http://calver.org/) `0Y.0M.MIC
 For upgrade instructions, please check the [migration guide](MIGRATIONS.released.md).
 
 ## Unreleased
-[Commits](https://github.com/scalableminds/webknossos/compare/24.05.0...HEAD)
+[Commits](https://github.com/scalableminds/webknossos/compare/24.07.0...HEAD)
 
 ### Added
-- Within the proofreading tool, the user can now interact with the super voxels of a mesh in the 3D viewport. For example, this allows to merge or cut super voxels from another. As before, the proofreading tool requires an agglomerate file. [#7742](https://github.com/scalableminds/webknossos/pull/7742)
-- Minor improvements for the timetracking overview (faster data loading, styling). [#7789](https://github.com/scalableminds/webknossos/pull/7789)
-- Updated several backend dependencies for optimized stability and performance. [#7782](https://github.com/scalableminds/webknossos/pull/7782)
-- Voxelytics workflows can be searched by name and hash. [#7790](https://github.com/scalableminds/webknossos/pull/7790)
-- If a self-hosted WEBKNOSSOS instance has not been updated for six months or more, a closable banner proposes an upgrade to webknossos.org. [#7768](https://github.com/scalableminds/webknossos/pull/7768)
-- Uploading an annotation into a dataset that it was not created for now also works if the dataset is in a different organization. [#7816](https://github.com/scalableminds/webknossos/pull/7816)
+- Added route `/import?url=<url_to_datasource>` to automatically import and view remote datasets. [#7844](https://github.com/scalableminds/webknossos/pull/7844)
+- The context menu that is opened upon right-clicking a segment in the dataview port now contains the segment's name. [#7920](https://github.com/scalableminds/webknossos/pull/7920) 
 
 ### Changed
-- Non-admin or -manager users can no longer start long-running jobs that create datasets. This includes annotation materialization and AI inferrals. [#7753](https://github.com/scalableminds/webknossos/pull/7753)
-- In the time tracking view, all annotations and tasks can be shown for each user by expanding the table. The individual time spans spent with a task or annotating an explorative annotation can be accessed via CSV export. The detail view including a chart for the individual spans has been removed. [#7733](https://github.com/scalableminds/webknossos/pull/7733)
-- Slightly refactored the `<FixExpandleTable/>`component to use columns as props. [#7772](https://github.com/scalableminds/webknossos/pull/7772)
-- The config value `datastore.localFolderWhitelist` can now be set for each datastore individually. [#7800](https://github.com/scalableminds/webknossos/pull/7800)
 
 ### Fixed
-- Fixed a bug where a toast that was reopened had a flickering effect during the reopening animation. [#7793](https://github.com/scalableminds/webknossos/pull/7793)
-- Fixed a bug where some annotation times would be shown double. [#7787](https://github.com/scalableminds/webknossos/pull/7787)
-- Fixed a bug where no columns were shown in the time tracking overview. [#7803](https://github.com/scalableminds/webknossos/pull/7803)
-- Fixed a bug where ad-hoc meshes for coarse magnifications would have gaps. [#7799](https://github.com/scalableminds/webknossos/pull/7799)
-- Fixed that the context menu didn't open correctly in the 3D viewport when right-clicking a node. [#7809](https://github.com/scalableminds/webknossos/pull/7809)
-- Fixed that right-clicking a mesh in the 3D viewport did crash when the corresponding segmentation layer was not visible. [#7811](https://github.com/scalableminds/webknossos/pull/7811)
 
 ### Removed
 

DEV_INSTALL.md

@@ -30,6 +30,7 @@ For non-localhost deployments, check out the [installation guide in the document
 * [node.js 18](http://nodejs.org/download/)
 * [yarn package manager](https://yarnpkg.com/)
 * [git](http://git-scm.com/downloads)
+* [cmake](https://cmake.org/download/)
 
 * For some development tasks like refreshing snapshots, Docker 19.03.0+ and Docker Compose 2.+ are required
 

MIGRATIONS.released.md

@@ -6,6 +6,27 @@ See `MIGRATIONS.unreleased.md` for the changes which are not yet part of an offi
 This project adheres to [Calendar Versioning](http://calver.org/) `0Y.0M.MICRO`.
 User-facing changes are documented in the [changelog](CHANGELOG.released.md).
 
+## [24.07.0](https://github.com/scalableminds/webknossos/releases/tag/24.07.0) - 2024-07-05
+[Commits](https://github.com/scalableminds/webknossos/compare/24.06.0...24.07.0)
+
+- The datastore config field `datastore.cache.dataCube.maxEntries` is no longer used and can be removed. [#7818](https://github.com/scalableminds/webknossos/pull/7818)
+- If your setup contains webknossos-workers, you may want to add the newly available job `align_sections` to the `supportedJobCommands` of your workers. Make sure you deploy the latest webknossos-worker release. [#7820](https://github.com/scalableminds/webknossos/pull/7820)
+- If you place WKW datasets directly on disk, a datasource-properties.json is now required, as WEBKNOSSOS no longer guesses its contents from the raw data. Standard dataset creation methods, e.g. with the WEBKNOSSOS CLI or python libs will already automatically this metadata file. [#7697](https://github.com/scalableminds/webknossos/pull/7697)
+
+### Postgres Evolutions:
+
+- [114-ai-models.sql](conf/evolutions/114-ai-models.sql)
+- [115-annotation-locked-by-user.sql](conf/evolutions/115-annotation-locked-by-user.sql)
+- [116-drop-overtimemailinglist.sql](conf/evolutions/116-drop-overtimemailinglist.sql)
+- [117-voxel-size-unit.sql](conf/evolutions/117-voxel-size-unit.sql)
+
+
+## [24.06.0](https://github.com/scalableminds/webknossos/releases/tag/24.06.0) - 2024-05-27
+[Commits](https://github.com/scalableminds/webknossos/compare/24.05.0...24.06.0)
+
+### Postgres Evolutions:
+None.
+
 ## [24.05.0](https://github.com/scalableminds/webknossos/releases/tag/24.05.0) - 2024-04-29
 [Commits](https://github.com/scalableminds/webknossos/compare/24.04.0...24.05.0)
 

MIGRATIONS.unreleased.md

@@ -6,6 +6,6 @@ This project adheres to [Calendar Versioning](http://calver.org/) `0Y.0M.MICRO`.
 User-facing changes are documented in the [changelog](CHANGELOG.released.md).
 
 ## Unreleased
-[Commits](https://github.com/scalableminds/webknossos/compare/24.05.0...HEAD)
+[Commits](https://github.com/scalableminds/webknossos/compare/24.07.0...HEAD)
 
 ### Postgres Evolutions: